Hi, does anyone use AnalyzeCovariates under GATK4.2.0.0? It seems that we should be able to perform BaseRecalibrator twice to get the -before and -after "recal_data.table" files and compare using AnalyzeCovariates. However, when I tried the following commands,
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# First BQSR (Already done)
# java -jar ${RJLJ}/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar \
# BaseRecalibrator \
# -R ${CKXLhg38} \
# -I ${ZLJ}/6_DedupedBam/${Takara_ID}_${Sample_Name}_aligned_fixmated_sorted_deduped.bam \
# --known-sites ${GATKFiles}/bundle/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz \
# --known-sites ${GATKFiles}/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
# --known-sites ${GATKFiles}/bundle/hg38/dbsnp_146.hg38.vcf.gz \
# -O ${ZLJ}/9_BQSRrecalDATAtable/${Takara_ID}_${Sample_Name}_merged_realigned_recal_data.table
# Second BQSR
java -jar ${RJLJ}/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar \
BaseRecalibrator \
-R ${CKXLhg38} \
-I ${ZLJ}/6_DedupedBam/${Takara_ID}_${Sample_Name}_aligned_fixmated_sorted_deduped.bam \
--known-sites ${GATKFiles}/bundle/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz \
--known-sites ${GATKFiles}/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
--known-sites ${GATKFiles}/bundle/hg38/dbsnp_146.hg38.vcf.gz \
-bqsr ${ZLJ}/9_BQSRrecalDATAtable/${Takara_ID}_${Sample_Name}_merged_realigned_recal_data.table*\
-O ${ZLJ}/9_BQSRrecalDATAtable/${Takara_ID}_${Sample_Name}_merged_realigned_recal_data.after.table
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I got an error saying that
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A USER ERROR has occurred: -bqsr is not a recognized option
***********************************************************************
So how can I get the -after "recal_data.table" file? Or is there any other method to perform quality check for bam files before going to variant calling?
Thanks in advance!
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# First BQSR (Already done)
# java -jar ${RJLJ}/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar \
# BaseRecalibrator \
# -R ${CKXLhg38} \
# -I ${ZLJ}/6_DedupedBam/${Takara_ID}_${Sample_Name}_aligned_fixmated_sorted_deduped.bam \
# --known-sites ${GATKFiles}/bundle/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz \
# --known-sites ${GATKFiles}/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
# --known-sites ${GATKFiles}/bundle/hg38/dbsnp_146.hg38.vcf.gz \
# -O ${ZLJ}/9_BQSRrecalDATAtable/${Takara_ID}_${Sample_Name}_merged_realigned_recal_data.table
# Second BQSR
java -jar ${RJLJ}/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar \
BaseRecalibrator \
-R ${CKXLhg38} \
-I ${ZLJ}/6_DedupedBam/${Takara_ID}_${Sample_Name}_aligned_fixmated_sorted_deduped.bam \
--known-sites ${GATKFiles}/bundle/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz \
--known-sites ${GATKFiles}/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
--known-sites ${GATKFiles}/bundle/hg38/dbsnp_146.hg38.vcf.gz \
-bqsr ${ZLJ}/9_BQSRrecalDATAtable/${Takara_ID}_${Sample_Name}_merged_realigned_recal_data.table*\
-O ${ZLJ}/9_BQSRrecalDATAtable/${Takara_ID}_${Sample_Name}_merged_realigned_recal_data.after.table
---------------------------------------------------------------------------------------------------------------------------------------------------------------
I got an error saying that
***********************************************************************
A USER ERROR has occurred: -bqsr is not a recognized option
***********************************************************************
So how can I get the -after "recal_data.table" file? Or is there any other method to perform quality check for bam files before going to variant calling?
Thanks in advance!